Hard-To-Undo Microbial Damage

Glenn had been on various antibiotics for cystic acne for seventeen years. His skin would initially respond well, but after a year or two the cystic lesions would return, and his dermatologist would switch him to a different antibiotic. Ten years after he first started taking antibiotics Glenn began to have persistent loose stools and weight loss. He experimented with cutting out dairy and tried to increase his calories, but no matter what he ate, he still had diarrhea and trouble gaining weight. Evaluation of his digestive tract eventually revealed a diagnosis of celiac disease, and he was put on a gluten free diet (GFD), which he adhered to strictly.

His doctor reassured Glenn that after a few months on the GFD his diarrhea and weight loss would improve, but two years later nothing had changed. Repeat evaluation showed the signs of celiac disease had completely resolved, and his small intestinal villi looked normal. But he didn’t feel normal at all. In addition to the diarrhea and difficulty putting on weight, he had numbness in his lower extremities, headaches, brain fog, fatigue, and a host of other symptoms that no one seemed able to explain. He was prescribed antidepressant and antianxiety drugs, which didn’t help and made him more tired. A shopping bag full of supplements prescribed by a local naturopath didn’t help either, and Glenn became more and more despondent about his health.

When Glenn came to see us, my nutritionist and I were particularly interested in what he was eating. The normal biopsies from his small intestine with no villus atrophy or other changes of active celiac disease suggested that inadvertent gluten exposure wasn’t the problem, but we wondered whether he might be one of those people with celiac disease who was eating a lot of gluten-free junk food. That wasn’t the case either. He was eating fruits and vegetables, nuts and seeds, legumes, brown rice, quinoa, and a little lean animal protein – not much room for improvement! I checked his stool for evidence of yeast overgrowth and that was negative, too. I examined the rest of Glenn’s digestive tract and found it all to be normal. Some microscopic forms of colitis can be associated with celiac disease, but he didn’t have any of them. Every test we did came back negative, except the IP test for leaky gut, which was markedly positive, suggesting a significant increase in the permeability or “leakiness” of his gut membrane, something associated with both celiac disease and microbial imbalance (dysbiosis).

We put Glenn on a number of different diets, including ninety days of a strict anti-yeast regimen that excludes most carbohydrates and is something I usually don’t recommend. We dosed him up with our most robust prescription-strength probiotic. We tried oil of oregano just in case he had a parasite we’d missed, and we pored over the results of his microbial stool analysis. In the end, it was clear that Glenn had severe dysbiosis, and no matter how we tried, we just couldn’t completely reverse it. Almost two decades of daily, heavy-duty, broad-spectrum antibiotics had decimated his gut flora, leading to autoimmune disease and chronic symptoms. He had some improvement with the interventions we recommended, but the majority of his symptoms were still present, and when last we heard from him he was contemplating entering a clinical trial of fecal transplantation for people with autoimmune diseases.

Most people with dysbiosis respond well to the regimen outlined in my Live Dirty, Eat Clean Plan, but there are times when microbial damage is simply too great to overcome. I’m optimistic that more novel and aggressive forms of microbiome rehabilitation, like fecal transplantation, will ultimately prove successful in refractory cases like Glenn’s. Of course, preventing serious dysbiosis by changing our medical practices – not treating acne with antibiotics as a prime example – is the ultimate goal, rather than trying to reverse damage that’s already been done.

Robynne Chutkan, MD, FASGE, is the founder of Gutbliss Rx. She is an integrative gastroenterologist and the bestselling author of Gutbliss, The Microbiome Solution, and The Bloat Cure. Educated at Yale and Columbia, she’s been on the faculty at Georgetown University Hospital since 1997 and is the founder of the Digestive Center for Wellness, an integrative gastroenterology practice incorporating microbiome analysis and nutritional counseling as part of the therapeutic approach to digestive disorders. An avid runner, snowboarder, and yogi, she is passionate about helping her patients live not just longer lives, but dirtier ones!

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